Have you notice whether you are getting any notifications during your beeping? Are you getting messages, calls, mail or calendar alarms?

Here is a section from the manual:

Notification icons report the arrival of new messages, calendar events, and alarms, as well as ongoing events, such as when call forwarding is on or the current call status.
When you receive a notification, its icon appears in the Status bar, along with a summary that appears only briefly. For a table of notification icons, see Notification icons. The trackball light also pulses once or repeatedly when you receive a new notification. See Sound & display settings.
You can open the Notifications panel to view a list of all your notifications. Depending on your settings and the model of your phone, you may also hear a notification sound, the phone may vibrate, and LEDs may blink.
Adjusting sound volume and other general notifications settings is described in Sound & display settings.
Applications whose activities produce notifications, such as Gmail and Google Talk, have their own settings, which you can use to configure whether and how they send notifications. See the sections on those applications for details.Perhaps it will lead you to find our if this is a real issue or just a setting or two.